RetrogeneDB ID: retro_pabe_1496

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 17:30226103..30226792(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: ADSS
• Ensembl ID: ENSPPYG00000000057
• Aliases: None
• Description: adenylosuccinate synthase [Source:HGNC Symbol;Acc:292]

Sequence

>retro_pabe_1496
GCGTTCGCCAAGAACTACCTGGAGGCATCCTCCCTGCCCAGCGGCGATTGCGGCCGCCCCAGGGCGCGGCCCGGAGGAAA
CCGGGTGACGGTGGTGCTCGGTGTGCAGTGGGGCGACGAAGGCAAAGGGGAGGTGGCGGATCTGCTGGCGTAGGACGCCG
TGTGCCGCTGCCAGGGAGGAAATAATGCTGGCCATACAGTTGTTGTGGATTCTGTGGAGTATGATTTTCATCTCTTACCC
AGTGAAATAATTATTCCAAATGTTACTGCATTCAATGGAAATGGTGTGGTAATTCATCTACCTGGATTGTTTGAAGAAGC
AGAGAAAAATGTTCAAAAAGGAAAAGGACTAGAAGGCTGGGAAAAAAGCTTATTTTATCTGACAGAGCTCATATTGTATT
TGATTTTCATCAAGCCGCTGATGGTGTCCAGGAACAACAGAGACAAGAACAAGCATGAAAAAATTTGGGTACAACAAAAA
AGGGCACTGGCCCAGTTTATTCTTCCAAAGCTGCTCGGAGTGGACTTAGGATGTGCGATCTTGTTTCTGACCTTGATAGC
TTCTCTGAGATGTTTAAAGTTCCAGCTAAACAATACAAATTTATACATCCCACTTTGGAAATAGACATTGAAGGTGAATT
ACAAAACCTCAAGGAAATTGGAGAATTATTACAAACAAGGGGTAGAGAG

Alignment

ORF - retro_pabe_1496 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.26 %
• Parental protein coverage: 50.88 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AFAETYPAASSLPNGDCGRARARPGGNRVTVVLGAQWGDEGKGKVVDLLAQDADIVCRCQGGNNAGHTVV
          AFA..Y..ASSLP.GDCGR.RARPGGNRVTVVLG.QWGDEGKG.V.DLLA.DA..VCRCQGGNNAGHTVV
Retrocopy AFAKNYLEASSLPSGDCGRPRARPGGNRVTVVLGVQWGDEGKGEVADLLA*DA--VCRCQGGNNAGHTVV

Parental  VDSVEYDFHLLPSGIINPNVTAFIGNGVVIHLPGLFEEAEKNVQKGKGLEGWEK-RLIISDRAHIVFDFH
          VDSVEYDFHLLPS.II.PNVTAF.GNGVVIHLPGLFEEAEKNVQKGKGLEGWEK..LI.SDRAHIVFDFH
Retrocopy VDSVEYDFHLLPSEIIIPNVTAFNGNGVVIHLPGLFEEAEKNVQKGKGLEGWEK<KLILSDRAHIVFDFH

Parental  QAADGIQEQQRQEQAGKNLGTTKKGIGPVYSSKAARSGLRMCDLVSDFDGFSERFKVLANQYKSIYPTLE
          QAADG.QEQQRQEQA.KNLGTTKKG.GPVYSSKAARSGLRMCDLVSD.D.FSE.FKV.A.QYK.I.PTLE
Retrocopy QAADGVQEQQRQEQA*KNLGTTKKGTGPVYSSKAARSGLRMCDLVSDLDSFSEMFKVPAKQYKFIHPTLE

Parental  IDIEGELQKLKGYMERIKPMVRD
          IDIEGELQ.LK...E......R.
Retrocopy IDIEGELQNLKEIGELLQTRGRE

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	25.54 RPM
SRP007412_cerebellum	0.00 RPM	21.65 RPM
SRP007412_heart	0.03 RPM	4.06 RPM
SRP007412_kidney	0.00 RPM	13.56 RPM
SRP007412_liver	0.00 RPM	9.61 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1496 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1496 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1496 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1826
Pan troglodytes	retro_ptro_1167

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017069	2 retrocopies	retro_cjac_2721, retro_cjac_452,
Homo sapiens	ENSG00000035687	1 retrocopy	retro_hsap_1826,
Monodelphis domestica	ENSMODG00000006559	1 retrocopy	retro_mdom_1431,
Oryctolagus cuniculus	ENSOCUG00000013982	1 retrocopy	retro_ocun_458,
Pongo abelii	ENSPPYG00000000057	1 retrocopy	retro_pabe_1496 ,
Pan troglodytes	ENSPTRG00000002178	1 retrocopy	retro_ptro_1167,